From 2cd6623aa0ddfe4e42b2d434e0523773bb3536ef Mon Sep 17 00:00:00 2001
From: Adam Novak
Date: Thu, 9 Apr 2020 15:52:23 -0700
Subject: Copy over/combine top-level project components

---
 Dockerfile              | 19 +++++++++++++++++++
 README.md               | 45 +++++++++++++++++++++++++++++++++++++++++++++
 bh20sequploader/main.py |  7 ++-----
 setup.py                |  6 +++++-
 4 files changed, 71 insertions(+), 6 deletions(-)
 create mode 100644 Dockerfile

diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..43fa8f2
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,19 @@
+# Dockerfile for containerizing the web interface
+FROM python:3.6-jessie
+WORKDIR /app
+
+RUN pip3 install gunicorn
+
+ADD LICENSE /app/
+ADD gittaggers.py /app/
+ADD setup.py /app/
+ADD README.md /app/
+ADD example /app/example
+ADD bh20seqanalyzer /app/bh20simplewebuploader
+ADD bh20sequploader /app/bh20sequploader
+ADD bh20simplewebuploader /app/bh20simplewebuploader
+
+RUN pip3 install -e .
+
+ENV PORT 8080
+CMD ["gunicorn", "-w", "4", "-b", "0.0.0.0:8080", "bh20simplewebuploader.main:app"]
diff --git a/README.md b/README.md
index a6fe052..4667310 100644
--- a/README.md
+++ b/README.md
@@ -159,4 +159,49 @@ odgi viz -i seqs.odgi -o seqs.png -x 4000 -y 500 -R -P 5
 
 For more information on building pangenome models, [see this wiki page](https://github.com/virtual-biohackathons/covid-19-bh20/wiki/Pangenome#pangenome-model-from-available-genomes).
 
+# Web Interface
+
+This project comes with a simple web server that lets you use the sequence uploader from a browser. It will work as long as you install the packager with the `web` extra.
+
+To run it locally:
+
+```
+virtualenv --python python3 venv
+. venv/bin/activate
+pip install -e .[web]
+env FLASK_APP=bh20simplewebuploader/main.py flask run
+```
+
+Then visit [http://127.0.0.1:5000/](http://127.0.0.1:5000/).
+
+## Production
+
+For production deployment, you can use [gunicorn](https://flask.palletsprojects.com/en/1.1.x/deploying/wsgi-standalone/#gunicorn):
+
+```
+pip3 install gunicorn
+gunicorn bh20simplewebuploader.main:app
+```
+
+This runs on [http://127.0.0.1:8000/](http://127.0.0.1:8000/) by default, but can be adjusted with various [gunicorn options](http://docs.gunicorn.org/en/latest/run.html#commonly-used-arguments)
+
+## GNU Guix
+
+To run the web uploader in a GNU Guix environment
+
+```
+guix environment guix --ad-hoc git python python-flask python-pyyaml nss-certs --network openssl -- env FLASK_APP=bh20simplewebuploader/main.py flask run
+```
+
+The containerized version looks like
+
+```
+guix environment -C guix --ad-hoc git python python-flask python-pyyaml nss-certs --network openssl
+```
+
+and
+
+```
+env FLASK_APP=bh20simplewebuploader/main.py flask run
+```
 
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py
index 8b8fefe..d3ebc0c 100644
--- a/bh20sequploader/main.py
+++ b/bh20sequploader/main.py
@@ -6,7 +6,6 @@ import json
 import urllib.request
 import socket
 import getpass
-from .qc_metadata import qc_metadata
 
 ARVADOS_API_HOST='lugli.arvadosapi.com'
 ARVADOS_API_TOKEN='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462'
@@ -20,8 +19,6 @@ def main():
 
     api = arvados.api(host=ARVADOS_API_HOST, token=ARVADOS_API_TOKEN, insecure=True)
 
-    qc_metadata(args.metadata.name)
-
     col = arvados.collection.Collection(api_client=api)
 
     print("Reading FASTA")
@@ -32,8 +29,8 @@ def main():
             f.write(r)
             r = args.sequence.read(65536)
 
-    print("Reading metadata")
-    with col.open("metadata.yaml", "w") as f:
+    print("Reading JSONLD")
+    with col.open("metadata.jsonld", "w") as f:
         r = args.metadata.read(65536)
         print(r[0:20])
         while r:
diff --git a/setup.py b/setup.py
index 48c25aa..41ace7b 100644
--- a/setup.py
+++ b/setup.py
@@ -16,6 +16,7 @@ except ImportError:
     tagger = egg_info_cmd.egg_info
 
 install_requires = ["arvados-python-client", "schema-salad"]
+web_requires = ["flask", "pyyaml"]
 
 needs_pytest = {"pytest", "test", "ptr"}.intersection(sys.argv)
 pytest_runner = ["pytest < 6", "pytest-runner < 5"] if needs_pytest else []
@@ -29,9 +30,12 @@ setup(
     author="Peter Amstutz",
     author_email="peter.amstutz@curii.com",
     license="Apache 2.0",
-    packages=["bh20sequploader", "bh20seqanalyzer"],
+    packages=["bh20sequploader", "bh20seqanalyzer", "bh20simplewebuploader"],
     package_data={"bh20sequploader": ["bh20seq-schema.yml"]},
     install_requires=install_requires,
+    extras_require={
+        'web': web_requires
+    },
     setup_requires=[] + pytest_runner,
     tests_require=["pytest<5"],
     entry_points={
-- 
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